The genetics Package

More documents

Recommendations

Info

42 write.pop.fileArgumentsdatafileData frame containing genotype objects to be exportedOutput filenamedigits Number of digits to use in numbering genotypes, either 2 or 3.description Description to use as the first line of the ’pop’ file.family, pid, father, motherVector of family, individual, father, and mother id’s, respectively.sexDetailsValuelocationVector giving the sex of the individual (1=Make, 2=Female)Location of the marker relative to the gene of interest, in base pairs.<strong>The</strong> format of ’Pop’ files is documented at http://wbiomed.curtin.edu.au/genepop/help_input.html, the format of ’pedigree’ files is documented at http://www.sph.umich.edu/csg/abecasis/GOLD/docs/pedigree.html and the format of ’marker’ files is documentedat http://www.sph.umich.edu/csg/abecasis/GOLD/docs/map.html.No return value.Author(s)See AlsoGregory R. Warnes 〈warnes@bst.rochester.edu〉write.tableExamples# TBA
Index∗Topic IOwrite.pop.file, 41∗Topic designpower.casectrl, 35∗Topic hplotplot.genotype, 34∗Topic manipexpectedGenotypes, 13groupGenotype, 21order.genotype, 31∗Topic miscci.balance, 8diseq, 10genotype, 14gregorius, 19groupGenotype, 21homozygote, 23HWE.chisq, 1HWE.exact, 3HWE.test, 4LD, 6locus, 25makeGenotypes, 29order.genotype, 31print.LD, 36summary.genotype, 39undocumented, 41==.genotype (genotype), 14==.haplotype (genotype), 14[.genotype (genotype), 14[.haplotype (genotype), 14[
Page 1 and 2: The genetics PackageFebruary 16, 20
Page 3 and 4: HWE.exact 3See AlsoHWE.exact, HWE.t
Page 5 and 6: HWE.test 5## S3 method for class 'd
Page 7 and 8: LD 7UsageLD(g1, ...)## S3 method fo
Page 9 and 10: ci.balance 9# Compute LD table for
Page 11 and 12: diseq 11Usagediseq(x, ...)## S3 met
Page 13 and 14: expectedGenotypes 13Examplesexample
Page 15 and 16: genotype 15DescriptionUsagegenotype
Page 17 and 18: genotype 17that appear in the data,
Page 19 and 20: genotype 19m4
Page 21 and 22: groupGenotype 21retval$missprobComp
Page 23 and 24: groupGenotype 23Examples## --- Setu
Page 25 and 26: homozygote 25Argumentsxgenotype obj
Page 27 and 28: locus 27is.marker(x)## S3 method fo
Page 29 and 30: makeGenotypes 29example.data
Page 31 and 32: makeGenotypes 31test1replace=TRUE),
Page 33 and 34: order.genotype 33ValueThe same as i
Page 35 and 36: power.casectrl 35See Alsogenotype,
Page 37 and 38: print.LD 37print.LDTextual and grap
Page 39 and 40: summary.genotype 39data
Page 41: undocumented 41Examplesexample.data
Page 45: INDEX 45write.marker.file(write.pop

The genetics Package

Create successful ePaper yourself

Delete template?

Save as template?